Methylation-specific MLPA (MS-MLPA): simultaneous detection of CpG methylation and copy number changes of up to 40 sequences

Copy number changes and CpG methylation of various genes are hallmarks of tumor development but are not yet widely used in diagnostic settings. The recently developed multiplex ligation-dependent probe amplification (MLPA) method has increased the possibilities for multiplex detection of gene copy number aberrations in a routine laboratory. Here we describe a novel robust method: the methylation-specific MLPA (MS-MLPA) that can detect changes in both CpG methylation as well as copy number of up to 40 chromosomal sequences in a simple reaction. In MS-MLPA, the ligation of MLPA probe oligonucleotides is combined with digestion of the genomic DNA–probe hybrid complexes with methylation-sensitive endonucleases. Digestion of the genomic DNA–probe complex, rather than double-stranded genomic DNA, allowed the use of DNA derived from the formalin treated paraffin-embedded tissue samples, enabling retrospective studies. To validate this novel method, we used MS-MLPA to detect aberrant methylation in DNA samples of patients with Prader–Willy syndrome, Angelman syndrome or acute myeloid leukemia.     

Atomic mapping of the interactions between the antiviral agent cyanovirin-N and oligomannosides by saturation-transfer difference NMR

The minimum oligosaccharide structure required for binding to the potent HIV-inactivating protein cyanovirin-N (CV-N) was determined by saturation-transfer difference (STD) NMR spectroscopy. Despite the low molecular mass of the protein (11 kDa), STD-NMR spectroscopy allowed the precise atomic mapping of the interactions between CV-N and various di- and trimannosides, substructures of Man-9, the predominant oligosaccharide on the HIV viral surface glycoprotein gp120. Contacts with mannosides containing the terminal Manalpha(1-->2)Manalpha unit of Man-9 were observed, while (1-->3)- and (1-6)-linked di- and trimannosides showed no interactions, demonstrating that the terminal Manalpha(1-->2)Manalpha structure plays a key role in the interaction. Precise epitope mapping revealed that, for Manalpha(1-->2)ManalphaOMe, Manalpha(1-->2)Manalpha(1-->3)ManalphaOMe, and Manalpha(1-->2)Manalpha(1-->6)ManalphaOMe, the protein is in close contact with H2, H3, and H4 of the nonreducing terminal mannose unit. In contrast, the STD-NMR spectrum of the CV-N/trisaccharide Manalpha(1-->2)Manalpha(1-->2)ManalphaOMe complex was markedly different, with resonances on all sugar units displaying equal enhancements, suggesting that CV-N is able to discriminate between the three structurally related trisaccharides.     

MAP kinase phosphatase 3 (MKP3) interacts with and is phosphorylated by protein kinase CK2alpha

Mitogen-activated protein (MAP) kinases play a central role in controlling a wide range of cellular functions following their activation by a variety of extracellular stimuli. MAP kinase phosphatases (MKPs) represent a subfamily of dual specificity phosphatases, which negatively regulate MAP kinases. Although ERK2 activity is regulated by its phosphorylation state, MKP3 is regulated by physical interaction with ERK2, independent of its enzymatic activity (Camps, M., Nichols, A., Gillieron, C., Antonsson, B., Muda, M., Chabert, C., Boschert, U., and Arkinstall, S., (1998) Science 280, 1262-1265; Farooq, A., Chaturvedi, G., Mujtaba, S., Plotnikova, O., Zeng, L., Dhalluin, C., Ashton, R., and Zhou, M. M. (2001), Mol. Cell 7, 387-399; Zhou, B., and Zhang, Z. Y. (1999) J. Biol. Chem. 274, 35526-35534). The interaction of ERK2 and MKP3 allows the reciprocal cross-regulation of their catalytic activity. Indeed, MKP3 acts as a negative regulator on ERK2-MAP kinase signal transduction activity, representing thus a negative feedback for this MAPK pathway. To identify novel proteins able to complex MKP3, we used the yeast two-hybrid system. Here we report that MKP3 and protein kinase CK2 form a protein complex, which can include ERK2. The phosphatase activity of MKP3 is then slightly increased in vitro, whereas in transfected cells, ERK2 dephosphorylation is reduced. In addition, we demonstrated that CK2 selectively phosphorylates MKP3, suggesting cross-regulation between CK2alpha and MKP3, as well as a modulation of ERK2-MAPK signaling by CK2alpha via MKP3.     

Analysis of genomic and expressed major histocompatibility class Ia and class II genes in a hexaploid Lake Tana African ‘large’ barb individual (<Emphasis Type="Italic">Barbus intermedius</Emphasis>)

Expression of too many co-dominant major histocompatibility complex (MHC) alleles is thought to be detrimental to proper functioning of the immune system. Polyploidy of the genome will increase the number of expressed MHC genes unless they are prone to a silencing mechanism. In polyploid Xenopus species, the number of MHC class I and II genes has been physically reduced, as it does not increase with higher ploidy genomes. In the zebrafish some class IIB loci have been silenced, as only two genomically bona fide loci, DAA/DAB and DEA/DEB, have been described. Earlier studies indicated a reduction in the number of genomic and expressed class II MHC genes in a hexaploid African large barb. This prompted us to study the number of MHC genes present in the genome of an African large barb individual (Barbus intermedius) in relation to those expressed, adopting the following strategy. Full-length cDNA sequences were generated from mRNA and compared with partial genomic class Ia and II sequences generated by PCR using the same primer set. In addition, we performed Southern hybridizations to obtain a verification of the number of class I and IIB genes. Our study revealed three ₂-microglobulin, five class Ia, four class IIA, and four class IIB genes at the genomic level, which were shown to be expressed in the hexaploid barb individual. The class Ia and class II data indicate that the ploidy status does not correlate with the presence and expression of these MHC genes.     

Magnitude of Cardiovascular Risk Factors in Rural and Urban Areas in Benin: Findings from a Nationwide Steps Survey

ObjectiveTo describe and compare the prevalences of CVRF in urban and rural populations of Benin.MethodsSubjects were drawn from participants in the Benin Steps survey, a nationwide cross-sectional study conducted in 2008 using the World Health Organisation (WHO) stepwise approach to surveillance of chronic disease risk factors. Subjects aged above 24 and below 65 years were recruited using a five-stage random sampling process within households. Sociodemographic data, behavioral data along with medical history of high blood pressure and diabetes mellitus were collected in Step 1. Anthropometric parameters and blood pressure were measured in Step 2. Blood glucose and cholesterol levels were measured in Step 3. CVRF were defined according to WHO criteria. The prevalences of CVRF were assessed and the relationships between each CVRF and the area of residence (urban or rural), were evaluated using multivariable logistic regression models.ResultsOf the 6762 subjects included in the study, 2271 were from urban areas and 4491 were from rural areas. High blood pressure was more prevalent in urban than in rural areas, 29.9% (95% confidence intervals (95% CI): 27.4, 32.5) and 27.5% (95% CI: 25.6, 29.5) respectively, p = 0.001 (p-value after adjustment for age and gender). Obesity was more prevalent in urban than in rural areas, 16.4% (95% CI: 14.4, 18.4) and 5.9% (95% CI: 5.1, 6.7), p<0.001. Diabetes was more prevalent in urban than in rural areas, 3.3% (95% CI: 2.1, 4.5) and 1.8% (95% CI: 1.2, 2.4), p = 0.004. Conversely, daily tobacco smoking was more prevalent in rural than in urban areas, 9.3% (95% CI: 8.1, 10.4) and 4.3% (95% CI: 3.1, 5.6), p<0.001. No differences in raised blood cholesterol were noted between the two groups.ConclusionAccording to our data, CVRF are prevalent among adults in Benin, and variations between rural and urban populations are significant. It may be useful to take account of the heterogeneity in the prevalence of CVRF when planning and implementing preventive interventions.     

Clinical tolerability of artesunate-amodiaquine versus comparator treatments for uncomplicated falciparum malaria: an individual-patient analysis of eight randomized controlled trials in sub-Saharan Africa

ABSTRACT: BACKGROUND: The widespread use of artesunate-amodiaquine (ASAQ) for treating uncomplicated malaria makes it important to gather and analyse information on its tolerability. METHODS: An individual-patient tolerability analysis was conducted using data from eight randomized controlled clinical trials conducted at 17 sites in nine sub-Saharan countries comparing ASAQ to other anti-malarial treatments. All patients who received at least one dose of the study drug were included in the analysis. Differences in adverse event (AE) and treatment emergent adverse event (TEAE) were analysed by Day 28. RESULTS: Of the 6,179 patients enrolled (74 % <5 years of age), 50 % (n = 3,113) received ASAQ, 20 % (n = 1,217) another ACT, and 30 % (n = 1,849) a non-ACT (combination or single-agent) treatment. Overall, 8,542 AEs were recorded. The proportion of patients experiencing at least one gastro-intestinal AE on ASAQ was 43 % (and higher than that with artemetherlumefantrine and dihydroartemisinin-piperaquine at two sites), and was 23 % for any other AEs (not different from other treatments). Specifically, the risk of diarrhoea, vomiting, cough and weakness was lower with artemether-lumefantrine; artemether-lumefantrine and dihydroartemisinin-piperaquine carried a higher risk of pruritus, chloroquine-SP had a higher risk of nausea. Parasitological recurrence increased the risk of occurrence of any AE. No other difference was detected. Comparing AE to TEAE in patients who had pre-treatment occurrence and grades of intensity recorded, AEs were significantly more related to the pretreatment prevalence of the symptom (p = 0.001, Fisher test); AEs overestimated TEAEs by a factor ranging from none to five-fold. The overall incidence of serious AEs (SAEs) with ASAQ was nine per 1,000 (29/3,113) and mortality was one per 1,000 (three deaths, none drug-related); both were similar to other treatments. CONCLUSION: ASAQ was comparatively well-tolerated. Safety information is important, and must be collected and analysed in a standardized way. TEAEs are a more objective measure of treatment-induced toxicity.     

Size of sampling unit strongly influences detection of seedling limitation in a wet tropical forest

Seedling limitation could structure communities, but often is evaluated with sampling units that are orders of magnitude smaller than mature plants. We censused seedlings for 5.5 years in five 1 × 200-m transects in a wet Neotropical forest. For 106 common species (≥ 10 seedlings in a transect), we calculated prevalence (occurrence of ≥ 1 newly emerged seedlings per sampling unit) at 1 m² and at 1 m × mature crown diameter units by aggregating adjacent quadrats. For most species, prevalence was 2–25% at 1 m², but 20–92% at mature crown scales. Increased prevalence arose from broadly distributed seedlings within transects, with unoccupied segments generally shorter than crown diameters. At the landscape scale, 69% of 301 species were locally rare (< 10 seedlings) and only 16% were represented in all transects (maximally separated by 2.4 km). Nonetheless, for more common species, much lower estimates of seedling limitation at mature crown scales suggest weaker influence of seedling limitation on community dynamics than previously assumed.     

Alterations in Bone and Erythropoiesis in Hemolytic Anemia: Comparative Study in Bled,Phenylhydrazine-Treated and Plasmodium-Infected Mice

Sustained erythropoiesis and concurrent bone marrow hyperplasia are proposed to be responsible for low bone mass density (BMD) in chronic hemolytic pathologies. As impaired erythropoiesis is also frequent in these conditions, we hypothesized that free heme may alter marrow and bone physiology in these disorders. Bone status and bone marrow erythropoiesis were studied in mice with hemolytic anemia (HA) induced by phenylhydrazine (PHZ) or Plasmodium infection and in bled mice. All treatments resulted in lower hemoglobin concentrations, enhanced erythropoiesis in the spleen and reticulocytosis. The anemia was severe in mice with acute hemolysis, which also had elevated levels of free heme and ROS. No major changes in cellularity and erythroid cell numbers occurred in the bone marrow of bled mice, which generated higher numbers of erythroid blast forming units (BFU-E) in response to erythropoietin. In contrast, low numbers of bone marrow erythroid precursors and BFU-E and low concentrations of bone remodelling markers were measured in mice with HA, which also had blunted osteoclastogenesis, in opposition to its enhancement in bled mice. The alterations in bone metabolism were accompanied by reduced trabecular bone volume, enhanced trabecular spacing and lower trabecular numbers in mice with HA. Taken together our data suggests that hemolysis exerts distinct effects to bleeding in the marrow and bone and may contribute to osteoporosis through a mechanism independent of the erythropoietic stress.